Skip to main content
PMC home page
Journal of Virology logoLink to Journal of Virology
. 1986 Sep;59(3):605–618. doi: 10.1128/jvi.59.3.605-618.1986

Functional domains within the a sequence involved in the cleavage-packaging of herpes simplex virus DNA.

L P Deiss, J Chou, N Frenkel
PMCID: PMC253218  PMID: 3016323

Abstract

Newly replicated herpes simplex virus (HSV) DNA consists of head-to-tail concatemers which are cleaved to generate unit-length genomes bounded by the terminally reiterated a sequence. Constructed defective HSV vectors (amplicons) containing a viral DNA replication origin and the a sequence are similarly replicated into large concatemers which are cleaved at a sequences punctuating the junctions between adjacent repeat units, concurrent with the packaging of viral DNA into nucleocapsids. In the present study we tested the ability of seed amplicons containing specific deletions in the a sequence to become cleaved and packaged and hence be propagated in virus stocks. These studies revealed that two separate signals, located within the Ub and Uc elements of the a sequence, were essential for amplicon propagation. No derivative defective genomes were recovered from seed constructs which lacked the Uc signal. In contrast, propagation of seed constructs lacking the Ub signal resulted in the selection of defective genomes with novel junctions, containing specific insertions of a sequences derived from the helper virus DNA. Comparison of published sequences of concatemeric junctions of several herpesviruses supported a uniform mechanism for the cleavage-packaging process, involving the measurement from two highly conserved blocks of sequences (pac-1 and pac-2) which were homologous to the required Uc and Ub sequences. These results form the basis for general models for the mechanism of cleavage-packaging of herpesvirus DNA.

Full text

PDF
605

Images in this article

607Image
on p.607
608Image
on p.608
610Image
on p.610
611Image
on p.611

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bankier A. T., Dietrich W., Baer R., Barrell B. G., Colbère-Garapin F., Fleckenstein B., Bodemer W. Terminal repetitive sequences in herpesvirus saimiri virion DNA. J Virol. 1985 Jul;55(1):133–139. doi: 10.1128/jvi.55.1.133-139.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Ben-Porat T., Tokazewski S. A. Replication of herpesvirus DNA. II. Sedimentation characteristics of newly synthesized DNA. Virology. 1977 Jun 15;79(2):292–301. doi: 10.1016/0042-6822(77)90356-7. [DOI] [PubMed] [Google Scholar]
  3. Chou J., Roizman B. Isomerization of herpes simplex virus 1 genome: identification of the cis-acting and recombination sites within the domain of the a sequence. Cell. 1985 Jul;41(3):803–811. doi: 10.1016/s0092-8674(85)80061-1. [DOI] [PubMed] [Google Scholar]
  4. Davison A. J. Structure of the genome termini of varicella-zoster virus. J Gen Virol. 1984 Nov;65(Pt 11):1969–1977. doi: 10.1099/0022-1317-65-11-1969. [DOI] [PubMed] [Google Scholar]
  5. Davison A. J., Wilkie N. M. Nucleotide sequences of the joint between the L and S segments of herpes simplex virus types 1 and 2. J Gen Virol. 1981 Aug;55(Pt 2):315–331. doi: 10.1099/0022-1317-55-2-315. [DOI] [PubMed] [Google Scholar]
  6. Deiss L. P., Frenkel N. Herpes simplex virus amplicon: cleavage of concatemeric DNA is linked to packaging and involves amplification of the terminally reiterated a sequence. J Virol. 1986 Mar;57(3):933–941. doi: 10.1128/jvi.57.3.933-941.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Hammerschmidt W., Ludwig H., Buhk H. J. Short repeats cause heterogeneity at genomic terminus of bovine herpesvirus 1. J Virol. 1986 Apr;58(1):43–49. doi: 10.1128/jvi.58.1.43-49.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Jacob R. J., Morse L. S., Roizman B. Anatomy of herpes simplex virus DNA. XII. Accumulation of head-to-tail concatemers in nuclei of infected cells and their role in the generation of the four isomeric arrangements of viral DNA. J Virol. 1979 Feb;29(2):448–457. doi: 10.1128/jvi.29.2.448-457.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Ladin B. F., Blankenship M. L., Ben-Porat T. Replication of herpesvirus DNA. V. Maturation of concatemeric DNA of pseudorabies virus to genome length is related to capsid formation. J Virol. 1980 Mar;33(3):1151–1164. doi: 10.1128/jvi.33.3.1151-1164.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Ladin B. F., Ihara S., Hampl H., Ben-Porat T. Pathway of assembly of herpesvirus capsids: an analysis using DNA+ temperature-sensitive mutants of pseudorabies virus. Virology. 1982 Jan 30;116(2):544–561. doi: 10.1016/0042-6822(82)90147-7. [DOI] [PubMed] [Google Scholar]
  11. Locker H., Frenkel N. BamI, KpnI, and SalI restriction enzyme maps of the DNAs of herpes simplex virus strains Justin and F: occurrence of heterogeneities in defined regions of the viral DNA. J Virol. 1979 Nov;32(2):429–441. doi: 10.1128/jvi.32.2.429-441.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Matsuo T., Heller M., Petti L., O'Shiro E., Kieff E. Persistence of the entire Epstein-Barr virus genome integrated into human lymphocyte DNA. Science. 1984 Dec 14;226(4680):1322–1325. doi: 10.1126/science.6095452. [DOI] [PubMed] [Google Scholar]
  13. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  14. Mocarski E. S., Deiss L. P., Frenkel N. Nucleotide sequence and structural features of a novel US-a junction present in a defective herpes simplex virus genome. J Virol. 1985 Jul;55(1):140–146. doi: 10.1128/jvi.55.1.140-146.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Mocarski E. S., Roizman B. Herpesvirus-dependent amplification and inversion of cell-associated viral thymidine kinase gene flanked by viral a sequences and linked to an origin of viral DNA replication. Proc Natl Acad Sci U S A. 1982 Sep;79(18):5626–5630. doi: 10.1073/pnas.79.18.5626. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Mocarski E. S., Roizman B. Site-specific inversion sequence of the herpes simplex virus genome: domain and structural features. Proc Natl Acad Sci U S A. 1981 Nov;78(11):7047–7051. doi: 10.1073/pnas.78.11.7047. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Mocarski E. S., Roizman B. Structure and role of the herpes simplex virus DNA termini in inversion, circularization and generation of virion DNA. Cell. 1982 Nov;31(1):89–97. doi: 10.1016/0092-8674(82)90408-1. [DOI] [PubMed] [Google Scholar]
  18. Poffenberger K. L., Roizman B. A noninverting genome of a viable herpes simplex virus 1: presence of head-to-tail linkages in packaged genomes and requirements for circularization after infection. J Virol. 1985 Feb;53(2):587–595. doi: 10.1128/jvi.53.2.587-595.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Preston V. G., Coates J. A., Rixon F. J. Identification and characterization of a herpes simplex virus gene product required for encapsidation of virus DNA. J Virol. 1983 Mar;45(3):1056–1064. doi: 10.1128/jvi.45.3.1056-1064.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Rao R. N., Rogers S. G. Plasmid pKC7: a vector containing ten restriction endonuclease sites suitable for cloning DNA segments. Gene. 1979 Sep;7(1):79–82. doi: 10.1016/0378-1119(79)90044-1. [DOI] [PubMed] [Google Scholar]
  21. Roizman B. The structure and isomerization of herpes simplex virus genomes. Cell. 1979 Mar;16(3):481–494. doi: 10.1016/0092-8674(79)90023-0. [DOI] [PubMed] [Google Scholar]
  22. Ryder K., Silver S., DeLucia A. L., Fanning E., Tegtmeyer P. An altered DNA conformation in origin region I is a determinant for the binding of SV40 large T antigen. Cell. 1986 Mar 14;44(5):719–725. doi: 10.1016/0092-8674(86)90838-x. [DOI] [PubMed] [Google Scholar]
  23. Spaete R. R., Frenkel N. The herpes simplex virus amplicon: a new eucaryotic defective-virus cloning-amplifying vector. Cell. 1982 Aug;30(1):295–304. doi: 10.1016/0092-8674(82)90035-6. [DOI] [PubMed] [Google Scholar]
  24. Spaete R. R., Frenkel N. The herpes simplex virus amplicon: analyses of cis-acting replication functions. Proc Natl Acad Sci U S A. 1985 Feb;82(3):694–698. doi: 10.1073/pnas.82.3.694. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Spaete R. R., Mocarski E. S. The alpha sequence of the cytomegalovirus genome functions as a cleavage/packaging signal for herpes simplex virus defective genomes. J Virol. 1985 Jun;54(3):817–824. doi: 10.1128/jvi.54.3.817-824.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Stow N. D. Localization of an origin of DNA replication within the TRS/IRS repeated region of the herpes simplex virus type 1 genome. EMBO J. 1982;1(7):863–867. doi: 10.1002/j.1460-2075.1982.tb01261.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Stow N. D., McMonagle E. C., Davison A. J. Fragments from both termini of the herpes simplex virus type 1 genome contain signals required for the encapsidation of viral DNA. Nucleic Acids Res. 1983 Dec 10;11(23):8205–8220. doi: 10.1093/nar/11.23.8205. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Szostak J. W., Orr-Weaver T. L., Rothstein R. J., Stahl F. W. The double-strand-break repair model for recombination. Cell. 1983 May;33(1):25–35. doi: 10.1016/0092-8674(83)90331-8. [DOI] [PubMed] [Google Scholar]
  29. Tamashiro J. C., Filpula D., Friedmann T., Spector D. H. Structure of the heterogeneous L-S junction region of human cytomegalovirus strain AD169 DNA. J Virol. 1984 Nov;52(2):541–548. doi: 10.1128/jvi.52.2.541-548.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Varmuza S. L., Smiley J. R. Signals for site-specific cleavage of HSV DNA: maturation involves two separate cleavage events at sites distal to the recognition sequences. Cell. 1985 Jul;41(3):793–802. doi: 10.1016/s0092-8674(85)80060-x. [DOI] [PubMed] [Google Scholar]
  31. Vlazny D. A., Frenkel N. Replication of herpes simplex virus DNA: localization of replication recognition signals within defective virus genomes. Proc Natl Acad Sci U S A. 1981 Feb;78(2):742–746. doi: 10.1073/pnas.78.2.742. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Vlazny D. A., Kwong A., Frenkel N. Site-specific cleavage/packaging of herpes simplex virus DNA and the selective maturation of nucleocapsids containing full-length viral DNA. Proc Natl Acad Sci U S A. 1982 Mar;79(5):1423–1427. doi: 10.1073/pnas.79.5.1423. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Wagner M. J., Summers W. C. Structure of the joint region and the termini of the DNA of herpes simplex virus type 1. J Virol. 1978 Aug;27(2):374–387. doi: 10.1128/jvi.27.2.374-387.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Wu H. M., Crothers D. M. The locus of sequence-directed and protein-induced DNA bending. Nature. 1984 Apr 5;308(5959):509–513. doi: 10.1038/308509a0. [DOI] [PubMed] [Google Scholar]

Articles from Journal of Virology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES